List of available PhD theses

Application of hydrodynamic cavitation in brewing

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Hydrodynamic cavitation (HC) is related to the phenomenon of formation, growth and collapse of bubbles occurring in an extremely small time interval causing intense release of energy at the point of bubble collapse. The collapse of microbubbles creates shock waves and a temporary increase in pressure and temperature at a large number of locations simultaneously. HK is a simple and energy efficient way to increase the intensity of interfacial phenomena. The aim of the thesis will be to identify technological steps (e.g. mashing, wort boiling, stabilization) in beer production, in which it will be possible to apply HK. Subsequently, the technological steps will be tested using HK and the impact of new processes on the analytical and sensory quality of beer will be quantified. These alternative processes will be compared with the traditional brewing process and the energy requirements for the individual process variants will be compared.

Comprehensive analysis of Monascus yellow and orange pigments for bioactivities

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The fungus Monascus belong to the ascomycetes, and the species Monascus purpureus is widely used in Asian countries as a microbial source of pigments. The polyketides produced by Monascus are therefore better known as food dyes and their biological activity has so far been studied extensively. The main goal of the work is to study in more detail various aspects of biological activity (e.g. antimicrobial, anticancerogenic, antidiabetic or antioxidant effects) of pure yellow and orange pigments or defined blends of Monascus metabolites and to focus on activities that have never been tested such as inhibitory effect on spore-forming bacteria. In addition, the synergistic effect of the pigments with standard antimicrobial drugs or antibiotics will also be tested. Thus, the proposed work may be useful in combating antibiotic resistance as a major obstacle in the treatment of infections. The work will also optimize the culture conditions for the overproduction of the desired, especially yellow pigments, in order to achieve their efficient production without simultaneous production of mycotoxin citrinin, which can be produced by certain strains of Monascus under certain conditions. Attention will also be paid to the development of a simple method of pigment isolation.

Enzymatic synthesis of metal nanoparticles with application potential

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Due to its outstanding physical-chemical properties, metal nanoparticles are the most widely produced types of nanomaterials with a wide application potential. The thesis will focus on the use of metabolism of microorganisms (bacteria and fungi) and plant extracts for intracellular and extracellular biosynthesis of metal nanoparticles, which exhibit antimicrobial activity in particular. Depending on the change in external conditions, the growth phase of the applied microorganism, and the type of metal precursor, wide possibilities for biosynthesis of new nanoparticles, which may have different size, shape and surface modification, are opened up. The nanoparticles obtained will be characterized by available physical techniques. The antimicrobial activity of the synthesized nanoparticles will be tested against selected opportunistically pathogenic microorganisms growing in suspension and biofilm.

Ethanol production from synthetic gas by autotrophic or mixotrophic bacteria

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Increasing emphasis on the use of waste within the so-called circular economy forces us to look for more environmentally friendly variants of conventional productions, which includes the effort to use carbon dioxide, one of the greenhouse gases as a suitable carbon source not only for plants and algae. The work deals with the production of ethanol by the so-called Wood-Ljungdahl metabolic pathway from synthesis gas, i.e. mixture containing CO, CO2 and H2 together with other minor components. Synthetic gas is obtained by gasification of biomass or other materials at high temperatures and its composition is variable depending on the starting material and the gasification method. The essence of the work will be the selection of a suitable strain capable of using this gaseous mixture as a carbon source. The use of selected species of Clostridium bacteria, such as Clostridium ljungdahlii or other genera, is assumed. In addition, the resistance of the selected strain to inhibitors resulting from gasification (tar, ammonia, cyanide, etc.) will be tested. Part of the thesis will also be the design of a suitable type of cultivation (batch with free or immobilized cells or continuous) and ideally also the transfer of the developed process from laboratory to pilot scale in cooperation with an industrial partner.

Interactions of flaviviral genomic RNA with viral proteins

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Flaviviruses are RNA viruses whose representatives, for example DENV, ZIKV, or TBEV, cause a variety of very serious illness. For successful replication within the infected cell, the flavivirus proteins must recognize and bind viral genomic RNA to assemble a nucleocapsid. The structural mechanisms leading to this step; however, remain unknown. The main objectives of this dissertation are (i) the characterization of the structural-functional motifs of flaviviral genomic RNA critical for the recognition, packaging and assembly of nucleocapsid, as well as (ii) the analysis of the flaviviral proteins involved in this process. For this purpose, a wide variety of modern experimental approaches will be used: molecular-genetic approaches such as cloning, PCR, mutagenesis to prepare DNA constructs, in vitro RNA transcription, expression of recombinant proteins in bacterial and mammalian cells, protein purification, immunoprecipitation associated with RNA sequencing (iCLIP), fluorescence anisotropy, optical tweezers technique, transmission electron microscopy and other.

Microbiome and metabolome based study of obesity, diabetes, and neurodegeneration and the therapeutic potential of prolactin-releasing peptide analogs by metabolomics

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It was well established that the gut microbiome contributes substantially to human health/disease status. Unfortunately, there is limited information about the underlying molecular mechanisms of gut microbiome-host crosstalk. Recent studies have suggested that gut microbiota play a fundamental role in diseases such as obesity, diabetes, cardiovascular and neurodegenerative diseases like Alzheimer’s disease. They are the world's leading causes of morbidity and mortality and are responsible for 60% of all deaths. It appears that obesity, type 2 diabetes (T2DM), and neurodegeneration have a common etiopathogenesis involving subclinical inflammation and insulin resistance.
The lumen of the gut is the biggest body surface facing the outer environment, and the mucosal immune system must be tightly regulated. The gut microbiota plays an important role in educating and modulating the host immune. Therefore, disturbance of the microbial ecosystem, called dysbiosis, substantially contributes to the establishment of the inflammatory state. We will use animal models of Alzheimer’s disease, where the modulation of the host immune system plays a crucial role. We assume that one of the mechanisms of how the gut microbiome associated with these conditions communicates with the immune system of the host is mediated by small molecular metabolites. The metabolites, which are usually identified as present in the gut and associated with pathologies, may be derived from the diet and/or are products of microbial metabolism. In the project, we will focus on interplay between disease development, microbiome and changes in metabolism to explore the development of the disease and efficacy of new lipidized analogs of the anorexigenic prolactin-releasing peptide as a complex therapy that simultaneously affects obesity, T2DM, and neurodegeneration in mouse and rat models.

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The structure of immature and mature HIV-1 particles are formed by the hexameric network of the same capsid protein (CA), but the intra- and inter-hexameric contacts are different for both types of particles. Any change in the stability of both types of these protein networks suppresses the replication ability of the virus and thus the infectivity of the virus. The critical role of CA in these steps of the HIV-1 replication cycle makes it a highly attractive pharmacological target.
In this work, we will study the effect of a number of different small molecules that by binding to CA substantially modulate the stability of both types of CA hexameric networks and thereby disrupt HIV-1 replication. In addition to specific synthetic molecules recently identified either in our laboratory or described in the literature, we will also study the role of small cellular cofactors whose mechanism of modulating the stability of the CA hexameric network in various retroviral species is unknown. Understanding the principle of positive and negative modulation of CA stability of hexameric networks of HIV-1 mature or immature particles may open a new therapeutic target for HIV-1 inhibition.

New possibilities for prediction of beer colloidal stability

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One of the limiting factors of beer stability is its colloidal stability. The colloidal stability of beer is determined by the composition of the colloidal system of beer and is influenced by other factors. The aim of this work is to find such methods of characterization of the colloidal system of beer that would allow us to predict its colloidal stability during the time. Another aim of the work is to find the reasons for reduced colloidal stability in different kinds of beers.

Possibilities of increasing beer foaming

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The most important characteristic of the Czech lager is its foam. The foam must have a certain appearance and stability. There are very important substances that create and support the foam and its stability. The aim of the thesis is to determine these substances and to test the possibilities of increasing their content. Attention will also be paid to substances that have a negative effect on the foam, their characterization and, possibly, decrease their content.

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Microorganisms use various regulatory mechanisms to control gene expression and phenotype formation. One of them is quorum sensing responding to fluctuations in cell population density. Mostly simple compounds, so-called signaling molecules, are involved in this type of regulation. Quorum sensing is often associated with the production of various virulence factors in both prokaryotic and eukaryotic microorganisms. The term quorum quenching is called a strategy to suppress quorum sensing and hence the virulence of many pathogens. The aim of this thesis is to find, deeper understanding and practical application of effective quorum quenching strategies for reducing or eliminating virulence, especially of pathogenic strains Pseudomonas aeruginosa and Candida albicans. The main attention will be paid to specific enzymes disrupting signal molecules, to substances interfering with these molecules and to participation of various type of nanoparticles.

Study of compounds interfering with regulatory mechanisms for biofilm formation of unicellular eukaryotes

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Microbial biofilms are single-species or in nature more often multi-species communities that are created by active adhesion / colonization of cells on the various types of surfaces, resulting in the formation of populations with a different phenotype. The biofilm populations are characterized by high resistance to environmental conditions. Extensive knowledge has been obtained particularly in the field of bacterial biofilms, including the regulation of their formation. In the case of eukaryotic single-celled microorganisms, the regulatory mechanisms of biofilm formation are less known and especially are focused on pathogenic strains of the genus Candida. The subject of this dissertation is to find natural or synthetic substances including nanoparticles, which will interfere with the regulatory mechanisms responsible for biofilm formation and stability in selected yeast and micromycetes. The result should be the tools and procedures to specifically affect the colonization of surfaces with studied microorganisms in medicine and various industries.

Study of different technologies for dry hopping of beer

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Dry hopping of beer is becoming very popular worldwide, and our breweries are also trying to use this technique. Dry hopping can be realized in a static and dynamic design and by using special aromatic hop varieties. The aim of this work is screening of the available, especially Czech hop varieties used for cold hopping and to compare the dry hopping and to select the appropriate regime of technology and equipment for small and large breweries.

The effect of natural preparations for plant nutrition and vitality on microbiological diversity and biotechnological potential of grapevine

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At present, there is a growing demand in agriculture for protective preparations manufactured from natural sources. This trend is related both to the expansion of ecological or biodynamic agriculture and to the efforts in the reduction of the use of chemical compounds that afflict the soil and the environment. The aim of the dissertation thesis is a cooperation in the development and testing of plant preparations that belong to the field of biodynamic agriculture. In selected preparations, the positive effects on the vitality of plants will be monitored. At the same time, these preparations will be characterized by quantitative and qualitative methods of chemical analysis. Another objective is to verify the effect of the application of these preparations on the natural microflora of grapes, whose composition and activity is essential for the successful realization of spontaneous vinification. Closely related to this point is the biotechnological analysis of fermentation (process dynamics, qualitative and quantitative changes within the microbial consortium, sensory comparison of the final product, etc.).

The effect of plant extracts and their biologically active substances on biofilms of opportunistic pathogens and commensal microorganisms

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Biofilms are communities of microorganisms, which play an important role in many aspects of human activities, including colonization of issues or implanted medical equipment and tools. Microbial biofilms are characterized by significantly different phenotype of their cells and by a wide range of interactions, both internal and external, including high resistance against unfavorable conditions or antimicrobial compounds. The aim of the dissertation thesis will be to study interactions of biologically active compounds of natural origin with microbial biofilms, including the possibility of synergistic effect resulting from the joint action of substances (e.g. complex plant extracts). Among the studied model microorganisms will be opportunistic pathogens, commensal and beneficial strains connected e.g. with the human digestive tract, with the emphasis on adhesion and biofilm formation. Included in the thesis will be characterization of the studied plant extracts, both the content of individual compounds and the overall properties (antioxidative activity etc.).

Use of a biodegradable carrier in biofilm reactors for production of extracellular enzymes

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The work is conducted under collaboration with Dekonta a.s. and with Institute of Macromolecular Chemistry of the AS CR, v.v.i., Prague that designs advanced microporous polyurethane foams with adjustable rate of biodegradation. Polyurethanes are synthesized as tailor-made polyester-ether polyols with different ratio of ether/ester segments to tune both appropriate hydrophilicity improving the adhesion of microorganisms and hydrolytic degradability.Polyurethane foam will be used as eco-friendly biofilm carrier and as primary or secondary source of carbon, energy and nitrogen for attached microorganisms in packed bed reactors for production of extracellular products e.g. enzymes. The research comprises evaluation of enzyme production and analytical evaluation of four basic processes of biological attract ofpolyurethanes:biodeterioration (FTIR and Ramanspectroscopy, SEM),biofragmentation (MALDI-TOF, HPLC-UV/RI, HPLC-MS and GC-MS), assimilation (Oxitop) and surface colonization (zeta potential, contact angle andimage analysis).

Use of non-traditional microorganisms in the production of beer

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Increasing market competition leads breweries to expand their product range. One possibility of new product development is the use of non-traditional microorganisms throughout the fermentation process. One such group of non-traditional microorganisms are probiotics, beneficial to human health, typically in improving immunity and maintaining the balance of intestinal microflora. The aim of the project will be to obtain a set of microorganisms with probiotic properties with the ability to ferment brewery wort and/or tolerate the environment of traditional and alcohol-free beers without reducing viability. In addition will be studied the fermentation capacity of selected microorganisms, the formation of flavor active compounds and the effect of the presence of non-traditional microorganisms on taste and colloidal stability of the products.

Wine waste as a source of biologically active substances for biotechnology

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Wine production is one of the oldest biotechnological processes. During the green works in the vineyard, grape processing and wine production, a significant amount of biological waste is produced, both in the form of plant biomass and microbial biomass. Grapevine is a well-researched crop from the point of view of the winemaking and biotechnological processes, but it is not sufficiently explored from the chemical point of view, i.e. from the point of view of exploitability of its intrinsic chemical components for further use. Individual types of waste originating in the vineyard or during the production can be a valuable source of e.g. biologically active substances. The subject of the dissertation thesis will be the use of biotechnologically usable compounds from wine wastes, both from conventional vineyards and from vineyards with a biodynamic approach. These may be e.g. biologically active substances, proanthocynidines from plant waste or the possibility of using wine lees.